Porcine circovirus type 2 (PCV2) genotyping in Austrian pigs in the years 2002 to 2017

Figures

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  Fig. 1. Maximum likelihood tree constructed with 105 capsid protein gene sequences. The tree is constructed from sequences of the present study (acc. no. MN150551-MN150684) and 32 representative PCV2 sequences of different genotypes (PCV2a labeled blue: acc. no. AF201305, AY424401, EU148507, EU386606, FJ483938, KP231099; PCV2b labeled red: acc. no. AY256457, DQ218419, EU545549, HQ591367, JN382175, KY806030, KY806064; PCV2c labeled turquoise: acc. no. EU148503; PCV2d labeled green: acc. no. JN006448, JF683408, JX912915; PCV2e labeled violet: acc. no. KT795288; PCV2f labeled orange: acc. no. HQ591381, KT369067, LC004746, LC004749, LC008134, MG739618; PCV2g labeled pink: acc. no. AY713470, DQ151643, JX948768, KP420197; PCV2h labeled brown: GQ449669, KC514969, KM042403, MH465473). NC_001792 served as outgroup. The tree with the highest log likelihood (− 3808.33) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches (1000 replicates, in %)

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  Fig. 2. Number of PCV2 sequences and haplotypes per genotype per year. The columns represent the numbers of PCV2 sequences per genotype per year (PCV2a – dark blue, PCV2b – dark red, PCV2d – dark green, PCV2g – pink) and the number of PCV2 haplotypes (HT) per genotype per year (PCV2a – light blue, PCV2b – light red, PCV2d – light green, PCV2g – rose)

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  Fig. 3. Median-joining networks of PCV2a, PCV2b and PCV2d classified according to the year of detection (see legend). The numbers of mutation steps are indicated in red numbers next to the branches. Branches without numbers represent mutation steps of one. A. PCV2a. Except of one haplotype, which is constituted of three samples, all haplotypes are constituted of one sample. The haplotypes are separated by one to 26 mutation steps from the main haplotype. B. PCV2b. One very common haplotype is shared by 34 individuals. Seven haplotypes are constituted of two to nine samples. Most haplotypes are constituted of one sample separated by one to two mutation steps from the main haplotype. Two further clades can be distinguished and the associated haplotypes are separated by up to twelve and 23 mutation steps, respectively, from the main haplotype. C. PCV2d. Except of three haplotypes, which are constituted of two to four samples, all haplotypes are constituted of one sample. The haplotypes are separated by one to two mutations steps from the main haplotype